[R-SIG-Mac] Error when fitting a brms model, maybe associated with Catalina MacOS
Manuel Spínola
m@p|no|@10 @end|ng |rom gm@||@com
Sun Dec 15 01:47:36 CET 2019
Yes Ken.
Manuel
On Sat, Dec 14, 2019 at 18:23 Ken Beath <ken using kjbeath.com.au> wrote:
> Did you install rstan last?
>
> Ken
>
> > On 15 Dec 2019, at 10:28 am, Manuel Spínola <mspinola10 using gmail.com>
> wrote:
> >
> > Dear list members,
> >
> > I updated everything, Catalina, Xcode, CLT, R 3.6.2, rstan from source,
> and installed the r-macos-rtools, but I still have problems.
> >
> > library(brms)
> > group <- rep(c("treat", "placebo"), each = 30)
> > symptom_post <- c(rnorm(30, mean = 1, sd = 2), rnorm(30, mean = 0, sd =
> 1))
> > dat1 <- data.frame(group, symptom_post)
> >
> > fit1 <- brm(bf(symptom_post ~ group, sigma ~ group),
> > data = dat1, family = gaussian())
> >
> > Chain 4: Iteration: 1 / 2000 [ 0%] (Warmup)
> > [1] "Error in sampler$call_sampler(args_list[[i]]) : "
> > [2] " c++ exception (unknown reason)"
> > error occurred during calling the sampler; sampling not done
> >
> >
> >
> >
> >
> >
> > El jue., 12 dic. 2019 a las 12:51, Balamuta, James Joseph (<
> balamut2 using illinois.edu>) escribió:
> > Greetings and Salutations All,
> >
> > Great to see the `r-macos-rtools` installer popping up! As the author of
> it, please note that it's an unofficial (non-CRAN backed) installer that
> seeks to automatically establish the CRAN toolchain in a friendly GUI
> installer. We developed it to help out students in STAT 385 @ UIUC [
> http://stat385.com/ ] setup the correct developer environment in a
> uniform manner as there wasn't really any prior installer packages made
> available at the time. We're grateful for the financial support that was
> given by Timothy Bates to sign the installer.
> >
> > With this being said, each step the installer takes is documented across
> a README file, installer splash screen, and by a post.
> >
> > README Overview:
> https://github.com/rmacoslib/r-macos-rtools#what-does-the-installer-do
> > Installer Splash:
> https://raw.githubusercontent.com/rmacoslib/r-macos-rtools/master/readme_img/lock_icon.png
> > Post:
> https://thecoatlessprofessor.com/programming/cpp/r-compiler-tools-for-rcpp-on-macos/
> >
> > That said, there is also Appendix C.3 macOS of R Installation and
> Administration [
> https://cran.r-project.org/doc/manuals/r-release/R-admin.html#macOS ]
> that goes over the details in greater depth.
> >
> > For those who are worried about security, please note that we've taken
> steps to ensure secure downloads by verifying the installer hashes prior to
> installing per prior remarks by Simon regarding earlier versions of the
> installer [ see the prior discussion and my response here:
> https://stat.ethz.ch/pipermail/r-sig-mac/2018-May/012745.html ].
> >
> > Lastly, and perhaps more critically, please note that just using Xcode
> CLI is not sufficient as it does not match the prescribed compilation
> toolchain (clang7 with OpenMP enabled and gfortran).
> >
> > Best,
> >
> > JJB
> >
> > On 12/11/19, 7:25 PM, "R-SIG-Mac on behalf of Manuel Spínola" <
> r-sig-mac-bounces using r-project.org on behalf of mspinola10 using gmail.com> wrote:
> >
> > An update.
> >
> > Before doing the suggested installation, I updated Catalina to
> 10.5.2,
> > Xtools to 11.3 and the Command Line Tools and it works.
> >
> > Manuel
> >
> > El mié., 11 dic. 2019 a las 16:05, Ken Beath (<ken using kjbeath.com.au>)
> > escribió:
> >
> > > No, it only downloads and installs the right compilers and updates
> > > Makevars and REnvirons. These are what Stan and RCpp require so
> you could
> > > do these manually.
> > >
> > > What it does is described at
> https://github.com/rmacoslib/r-macos-rtools
> > >
> > > Ken
> > >
> > > > On 12 Dec 2019, at 1:14 am, Manuel Spínola <mspinola10 using gmail.com>
> wrote:
> > > >
> > > > Thank you very much to all.
> > > >
> > > > Does Installing the macos-rtools could affect R in other ways?
> > > >
> > > > Manuel
> > > >
> > > > El mié., 11 dic. 2019 a las 6:56, Ken Beath (<ken using kjbeath.com.au
> >)
> > > escribió:
> > > > What worked for me was installing the tools using
> > > https://github.com/rmacoslib/r-macos-rtools/releases
> > > >
> > > > and then installing rstan from source ie
> > > install.packages(“rstan”,type=“source) as suggested on one of the
> stan
> > > forums
> > > >
> > > > Ken
> > > >
> > > > > On 11 Dec 2019, at 11:09 am, Manuel Spínola <
> mspinola10 using gmail.com>
> > > wrote:
> > > > >
> > > > > Dear list members,
> > > > >
> > > > > When trying to fit this example from the CRAN repository fro
> brms, I
> > > got
> > > > > the following error message after the 4th chain. I am using R
> 3.6.1 in
> > > > > Catalina MacOS.
> > > > >
> > > > >
> > > > > library(brms)
> > > > >
> > > > > group <- rep(c("treat", "placebo"), each = 30)
> > > > > symptom_post <- c(rnorm(30, mean = 1, sd = 2), rnorm(30, mean
> = 0, sd
> > > = 1))
> > > > > dat1 <- data.frame(group, symptom_post)
> > > > >
> > > > > fit1 <- brm(bf(symptom_post ~ group, sigma ~ group),
> > > > > data = dat1, family = gaussian())
> > > > >
> > > > >
> > > > > [1] "Error in sampler$call_sampler(args_list[[i]]) : "
> > > > > [2] " c++ exception (unknown reason)"
> > > > > error occurred during calling the sampler; sampling not done
> > > > >
> > > > > I think is a problem with Catalina MacOS, but I don´t know how
> to
> > > solve it.
> > > > >
> > > > > Manuel
> > > > >
> > > > > --
> > > > > *Manuel Spínola, Ph.D.*
> > > > > Instituto Internacional en Conservación y Manejo de Vida
> Silvestre
> > > > > Universidad Nacional
> > > > > Apartado 1350-3000
> > > > > Heredia
> > > > > COSTA RICA
> > > > > mspinola using una.cr <mspinola using una.ac.cr>
> > > > > mspinola10 using gmail.com
> > > > > Teléfono: (506) 8706 - 4662
> > > > > Personal website: Lobito de río <
> > > https://sites.google.com/site/lobitoderio/>
> > > > > Institutional website: ICOMVIS <http://www.icomvis.una.ac.cr/>
> > > > >
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> > > > >
> > > > > _______________________________________________
> > > > > R-SIG-Mac mailing list
> > > > > R-SIG-Mac using r-project.org
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> > > > >
> > > >
> > > >
> > > >
> > > > --
> > > > Manuel Spínola, Ph.D.
> > > > Instituto Internacional en Conservación y Manejo de Vida
> Silvestre
> > > > Universidad Nacional
> > > > Apartado 1350-3000
> > > > Heredia
> > > > COSTA RICA
> > > > mspinola using una.cr
> > > > mspinola10 using gmail.com
> > > > Teléfono: (506) 8706 - 4662
> > > > Personal website: Lobito de río
> > > > Institutional website: ICOMVIS
> > >
> > >
> >
> > --
> > *Manuel Spínola, Ph.D.*
> > Instituto Internacional en Conservación y Manejo de Vida Silvestre
> > Universidad Nacional
> > Apartado 1350-3000
> > Heredia
> > COSTA RICA
> > mspinola using una.cr <mspinola using una.ac.cr>
> > mspinola10 using gmail.com
> > Teléfono: (506) 8706 - 4662
> > Personal website: Lobito de río <
> https://sites.google.com/site/lobitoderio/>
> > Institutional website: ICOMVIS <http://www.icomvis.una.ac.cr/>
> >
> > [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > R-SIG-Mac mailing list
> > R-SIG-Mac using r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> >
> >
> >
> >
> > --
> > Manuel Spínola, Ph.D.
> > Instituto Internacional en Conservación y Manejo de Vida Silvestre
> > Universidad Nacional
> > Apartado 1350-3000
> > Heredia
> > COSTA RICA
> > mspinola using una.cr
> > mspinola10 using gmail.com
> > Teléfono: (506) 8706 - 4662
> > Personal website: Lobito de río
> > Institutional website: ICOMVIS
>
> --
*Manuel Spínola, Ph.D.*
Instituto Internacional en Conservación y Manejo de Vida Silvestre
Universidad Nacional
Apartado 1350-3000
Heredia
COSTA RICA
mspinola using una.cr <mspinola using una.ac.cr>
mspinola10 using gmail.com
Teléfono: (506) 8706 - 4662
Personal website: Lobito de río <https://sites.google.com/site/lobitoderio/>
Institutional website: ICOMVIS <http://www.icomvis.una.ac.cr/>
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